Phenotypes

This web page was produced as an assignment for Gen677 at UW-Madison Spring 2009.

Gene Ontology

AmiGO

The information below is from the GO Consortium, and is a listing of the GO terms for NrCAM. There are 13 listings, 8 of which are biological process terms that focus on the development of the central nervous system and brain development. Processes such as axonal growth/formation as well as sodium channel development and synaptogenesis are important GO terms as they offer information about why NrCAM is a nice target for autism research. These results were about what I expected before doing my searches as I knew the gene was heavily implicated in brain and central nervous system development. I got an idea about the specificity of the gene's role in brain/CNS development, it appears to play a significant role in the formation of neural networks which depend on axon extension, cell-cell adhesion, and synaptogenesis. The ankyrin and protein binding molecular functions support the possibility that NrCAM is involved in cell-cell adhesion as ankyrin is a plasma membrane protein involved in cell-cell binding. This cell-cell (neuron-neuron) interaction is very important in setting up neuronal networks, and its implications in autism are logical as autistic individuals have defects in several neuronal functions. These functions are all supportive of the predicted localization of NrCAM to the plasma membrane which is also predicted by gene ontology; NrCAM is integral to the plasma membrane and present on the external side of the plasma membrane according to AmiGO.

From AmiGO. 2009. NrCAm gene ontology. Retrieved from http://amigo.geneontology.org/cgi-bin/amigo/
gp-details.cgi?gp=UniProtKB:Q92823&session_id=6078amigo1242246699.

GOA

I attempted to use the Gene Ontology Annotation (GOA) database to find information about NrCAM's gene ontology, however my searches did not return any results as NrCAM had not been annotated according to the database.

C. elegans WormBase

The C. elegans NrCAM homologue, LAD-1, was used to search for RNAi knockdown phenotypes in C. elegans.

WormBase provides a wide range of entries when doing gene searches. The information includes gene ontology, expression maps in C. elegans, and gene homology information in addition to RNAi experimental data. From the database, I will only provide information related to observed phenotypes in RNAi experiments.

WormBase returned three phenotypes seen in RNAi experiments as seen in Table 1 below. Experimental data can be viewed by clicking on the individual phenotypes in the table which link out to the publications as well as general information about the experiments. The abnormal axon trajectory phenotype is interesting and is concistent with the gene ontology data presented above. This provides support for the research of NrCAM in autism as the development of neuronal networks seems to be abnormal in individuals with autism. Also, the lethal phenotype also speaks to the importance of the LAD-1 gene and protein in C. elegans.

Table 1. These phenotypes were seen by knocking down LAD-1 using RNAi. Click on the table to view the WormBase data.

WormBase also provides experimental evidence which do not result from LAD-1 RNAi knockdowns as seen below in Table 2. This information can be as important as the information in Table 1 as it might allow researchers to eliminate possiblilities that are not affected by the gene. This will promote more focused research on functions that can be inhibited with LAD-1 knockdowns.

Table 2. WormBase included phenotypes that were not observed in RNAi experiments. Click on the table to view the WormBase data.

RNAi Database

RNAi Database did not return any LAD-1 knockdown experiments in C. elegans. There was one result for Sax-7, an L1CAM orthologue, but this entry was not well annotated and I did not include it in my analysis.

D. melanogaster RNAi database: Drosophila RNAi Screening Center

I searched the Drosophila RNAi databases including the Drosophila RNAi Screening Center and was not able to find neuroglain (Nrg), the NrCAM homologue, RNAi phenotypes in any screens. This was also the case when I looked at FlyBase. I was surprised that there were not any Nrg RNAi experiments returned as it is an important protein in Drosophila as well.

Analysis

The LAD-1 RNAi experiments and phenotypes returned by WormBase were very interesting considering what we know about NrCAM's proposed role in axon guidance and development of neuronal networks. The phenotypes in Table 1, specifically abnormal axon trajectory, supports these proposed roles and the lethal phenotype highlights the importance of the protein during development. I think more RNAi experiments in C. elegans are woth being conducted and will allow scientists to gain further evidence and information about the role of the protein in the development of the nervous system. I would also like to see some experiments conducted in Drosophila, looking at neuroglian knockdown phenotypes in order to gain more support for the functionality of the NrCAM protein in humans.

Brett Maricque
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Last updated: 5/13/09
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